Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_084931715.1 HA51_RS02580 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_002095475.1:WP_084931715.1 Length = 234 Score = 147 bits (371), Expect = 2e-40 Identities = 83/215 (38%), Positives = 126/215 (58%), Gaps = 7/215 (3%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L++ + + Y I L ++ V ++G NG GK+TL+ TI G A GS+ Sbjct: 1 MLEIKEMVSGYNKIPVLHLSELFVGAKSFTGVLGRNGMGKTTLLRTIMGELPAWQGSIAL 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAED---VEKIF 127 G DITR H+ A I P+GR+IFP +TV ENL+MG +KHF+ +E++ Sbjct: 61 NGIDITRYQAHQRAVAGIGFVPQGRQIFPLLTVEENLRMGC----VKHFSRAGTIIEQML 116 Query: 128 TLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIR 187 +FPRLK Q GG LSGGEQQ+L++ R L +P+L+LLDEP+ G+ P I + I E ++ Sbjct: 117 EIFPRLKRLLTQPGGALSGGEQQLLALARCLCGQPQLVLLDEPTEGIQPNICEEIIETLQ 176 Query: 188 KLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKV 222 +L +++ LVEQ+ LS R +V+ G++ Sbjct: 177 RLRHEMDISIILVEQDIEFLYALSDRIHVIEKGQI 211 Lambda K H 0.320 0.137 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 174 Number of extensions: 13 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 247 Length of database: 234 Length adjustment: 23 Effective length of query: 224 Effective length of database: 211 Effective search space: 47264 Effective search space used: 47264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory